**2.2. Inter- and intramolecular hydrogen bonds in the crystal structure of organic compounds**

Hydrogen bond plays a key and major role in the biological and pharmaceutical systems and remains a topic of intense current interest. Few selected recent articles exemplify the general scope of the topic, ranging from the role of H-bonding such as in: weak interaction in gas phase "(Nishio, 2005; Wang et al., 2005)", supramolecular assemblies "(McKinlay et al., 2005)", helical structures "(Azumaya et al., 2004; Noroozi Pesyan, 2010)". Important consequences of both inter- and intra-molecular H-bonding have long been recognized in the physicochemical behavior of DNA and RNA "(Jeffery & Saenger, 1991)".

Several kinds of hydrogen bond have been reported. If the donor-acceptor distance to be in the range of; 2.50 ≤ d (O O) ≤ 2.65, this kind of hydrogen bond is strong and when shorter than 2.50 Å (d(O O)≤ 2.50), to be very strong hydrogen bond "(Gilli et al., 1994)".

In very short O H O bonds (2.40-2.45 Å) the major distribution of the proton are as follows:


For instance, the structure of the potassium hydrogen dichloromaleate (**26**) has been studied by neutron diffraction at 30 and 295 K, with the emphasis on the location of the protons. There are two crystallographically independent hydrogen atoms in two very short hydrogen bonds, 2.437(2) and 2.442(2) Å at 30 K. For the centrosymmetric space group P1, with the hydrogen atoms located at the centres of symmetry, the structure could be refined successfully. Olovsson et al. have then been applied several different types of refinements on this structure, including unconventional models; with all atoms except hydrogen constrained in P1, but with hydrogen allowed to refine without any constraints in P1, anisotropic refinement of all atoms resulted in clearly off-centred hydrogen positions. The shifts of the two hydrogen atoms from the centres of symmetry are 0.15(1) and 0.12(1) Å, respectively, at 30 K, and 0.15(1) Å for both hydrogen atoms at room temperature. At 30 K: R(F) = 0.036 for 1485 reflections; at 295 K: R(F) = 0.035 for 1349 reflections (Olovsson et al., 2001)" (Fig. 11).

One of the most interesting example about intermolecular hydrogen bond is the heptan-4-yl (2'-hydroxy-[1,1'-binaphthalen]-2-yl) phosphonate (**27a**) "(Dabbagh et al., 2007)". The phosphonate **27a** was existed in dimmer form via two strong intermolecular hydrogen bonds with centrocymmetric (*Ci*) 18-membered dimmer form consisting of two monomers strongly hydrogen-bonded between the oxygen of P=O units and hydroxyl hydrogen atoms (Fig. 12). The crystal structure of **27a** was determined by X-ray crystallography and is shown

**Figure 11.** Crystal structure of potassium hydrogen dichloromaleate (**26**).

**Figure 12.** Crystal structure of **27a**.

202 Recent Advances in Crystallography

**compounds** 

follows:

2001)" (Fig. 11).

**2.2. Inter- and intramolecular hydrogen bonds in the crystal structure of organic** 

Hydrogen bond plays a key and major role in the biological and pharmaceutical systems and remains a topic of intense current interest. Few selected recent articles exemplify the general scope of the topic, ranging from the role of H-bonding such as in: weak interaction in gas phase "(Nishio, 2005; Wang et al., 2005)", supramolecular assemblies "(McKinlay et al., 2005)", helical structures "(Azumaya et al., 2004; Noroozi Pesyan, 2010)". Important consequences of both inter- and intra-molecular H-bonding have long been recognized in

Several kinds of hydrogen bond have been reported. If the donor-acceptor distance to be in the range of; 2.50 ≤ d (O O) ≤ 2.65, this kind of hydrogen bond is strong and when shorter

In very short O H O bonds (2.40-2.45 Å) the major distribution of the proton are as

For instance, the structure of the potassium hydrogen dichloromaleate (**26**) has been studied by neutron diffraction at 30 and 295 K, with the emphasis on the location of the protons. There are two crystallographically independent hydrogen atoms in two very short hydrogen bonds, 2.437(2) and 2.442(2) Å at 30 K. For the centrosymmetric space group P1, with the hydrogen atoms located at the centres of symmetry, the structure could be refined successfully. Olovsson et al. have then been applied several different types of refinements on this structure, including unconventional models; with all atoms except hydrogen constrained in P1, but with hydrogen allowed to refine without any constraints in P1, anisotropic refinement of all atoms resulted in clearly off-centred hydrogen positions. The shifts of the two hydrogen atoms from the centres of symmetry are 0.15(1) and 0.12(1) Å, respectively, at 30 K, and 0.15(1) Å for both hydrogen atoms at room temperature. At 30 K: R(F) = 0.036 for 1485 reflections; at 295 K: R(F) = 0.035 for 1349 reflections (Olovsson et al.,

One of the most interesting example about intermolecular hydrogen bond is the heptan-4-yl (2'-hydroxy-[1,1'-binaphthalen]-2-yl) phosphonate (**27a**) "(Dabbagh et al., 2007)". The phosphonate **27a** was existed in dimmer form via two strong intermolecular hydrogen bonds with centrocymmetric (*Ci*) 18-membered dimmer form consisting of two monomers strongly hydrogen-bonded between the oxygen of P=O units and hydroxyl hydrogen atoms (Fig. 12). The crystal structure of **27a** was determined by X-ray crystallography and is shown

ii. The proton is located precisely at the centre (symmetric or centred hydrogen bond). iii. There is statistically disorder of the proton between two positions on either side of the centre (the proton is closer to one or the other side in different domains of the crystal). iv. There is a dynamical disorder between two positions as in (iii); the proton jumps between the two positions in the same hydrogen bond "(Gilli et al., 1994; P. Gilli & G.

the physicochemical behavior of DNA and RNA "(Jeffery & Saenger, 1991)".

i. The proton is closer to one of the O atoms (asymmetric hydrogen bond).

Gilli, 2000; Olovsson et al., 2001; Steiner, 2002)".

than 2.50 Å (d(O O)≤ 2.50), to be very strong hydrogen bond "(Gilli et al., 1994)".

**Figure 13.** Representatively**,** two strong intermolecular hydrogen bonds with centrocymmetric 18 membered dimmer form in **27a** and **27b**.

in Fig. 12. The selected bond lengthes, angles and torsion angles of **27a** are summarized in Tables 2-4, respectively. Crystal data indicated the torsion angles (*φ*) between two naphthalenic rings moieties in BINOL species are 95.28(16)° and are transoid forms (Fig. 13). The intermolecular hydrogen bond distance in the structure of **27a** was obtained 2.70 Å (strong hydrogen bond) and comparised with other hydrogen bonds P-containing systems (Table 5).


**Table 2.** Selected bond length (Å) of dimmer **27a**.


**Table 3.** Selected bond angle of dimmer **27a**.


**Table 4.** Selected torsion angles of dimmer **27a**.

204 Recent Advances in Crystallography

**Table 2.** Selected bond length (Å) of dimmer **27a**.

**Table 3.** Selected bond angle of dimmer **27a**.

in Fig. 12. The selected bond lengthes, angles and torsion angles of **27a** are summarized in Tables 2-4, respectively. Crystal data indicated the torsion angles (*φ*) between two naphthalenic rings moieties in BINOL species are 95.28(16)° and are transoid forms (Fig. 13). The intermolecular hydrogen bond distance in the structure of **27a** was obtained 2.70 Å (strong hydrogen bond) and comparised with other hydrogen bonds P-containing systems (Table 5).

> Entry Bond length (Å) 1 P(1) – O(3) 1.4578(11) 2 P(1) – O(2) 1.5544(12) 3 P(1) – O(1) 1.5865(11) 4 P(1) – H(1) 1.295(16) 5 O(1) – C(1) 1.4073(17) 6 O(2) – C(21) 1.5006(19) 7 O(4) – C(12) 1.3634(18) 8 O(4) – H(4) 0.89(2) 9 O(3) – H(4) 1.81(2) 10 C(10) – C(11) 1.4942(19)

> Entry Bond Angle (*θ*, °) 1 O(3) – P(1) – O(2) 118.32(7) 2 O(3) – P(1) – O(1) 113.50(7) 3 O(2) – P(1) – O(1) 102.16(6) 4 O(3) – P(1) – H(1) 112.7(7) 5 O(2) – P(1) – H(1) 103.9(7) 6 O(1) – P(1) – H(1) 104.7(8) 7 C(1) – O(1) – P(1) 122.24(9) 8 C(21) – O(2) – P(1) 122.27(10) 9 C(12) – O(4) – H(4) 114.4(14) 10 C(10) – C(1) – C(2) 123.47(14) 11 C(10) – C(1) – O(1) 117.78(13) 12 C(2) – C(1) – O(1) 118.66(13) 13 C(9) – C(10) – C(11) 120.98(12) 14 O(4) – C(12) – C(11) 124.08(14) 15 O(4) – C(12) – C(13) 114.68(13) 16 O(2) – C(21) – C(22) 107.92(12) 17 O(2) – C(21) – C(25) 111.86(18) 18 C(22) – C(21) – C(25) 108.84(18) 19 O(2) – C(21) – H(21) 109.4 20 C(22) – C(21) – H(21) 109.4 21 C(25) – C(21) – H(21) 109.4


Data taken from references "(Corbridge, 1990; Gilli et al., 1994; Gilli & & Gilli, 2000; Steiner, 2002)".

**Table 5.** Classification of hydrogen bonds within P-containing systems.

Dimeric centrosymmetric ring structures are quite common within phosphorous chemistry: for example; the structures of **28** and **29** are of 12- and 8-membered structures, respectively "(Corbridge, 1990)". According to spectroscopic evidence, esters of (trichloroacetyl) amidophosphoric acid (**29**) exist as **29I** rather than **29II**, which suggests that the hydrogen bond in N-H O=P is stable than that of in N-H O=C "(Corbridge, 1990)".

The formula structures of (*E*)-2-benzamido-3-(pyridin-2-yl)acrylic acid (**30a**) and (*E*)-2 benzamido-3-(pyridin-4-yl)acrylic acid (**30b**) are shown in Figure 14. The isomer **30a** possesses a strong seven-membered ring intramolecular hydrogen bonding and shows quite different physicochemical properties, such as solubility and pKa, comparing with its isomer **30b**. The pconjugation between pyridyl and acrylate moieties is extended by intramolecular hydrogen bonding leading to a strong absorption at about 340 nm. Intramolecular proton transfer facilitates in the excited state, resulting in dual emission at around 420 nm and 490 nm in acetonitrile "(Guo et al., 2011)". Crystal structure of **30a** show a strong seven-membered ring intramolecular hydrogen bonding (Figure 15). The intramolecular proton transfer is facilitated by intramolecular hydrogen bond of O–H N. Tautomeric forms of **30a** is shown in Scheme 8.

**Figure 14.** Formula structures of **30a** and **30b**.

**Figure 15.** Crystal structure of **30a**.

206 Recent Advances in Crystallography

Dimeric centrosymmetric ring structures are quite common within phosphorous chemistry: for example; the structures of **28** and **29** are of 12- and 8-membered structures, respectively "(Corbridge, 1990)". According to spectroscopic evidence, esters of (trichloroacetyl) amidophosphoric acid (**29**) exist as **29I** rather than **29II**, which suggests that the hydrogen

O

H

H

**28**

The formula structures of (*E*)-2-benzamido-3-(pyridin-2-yl)acrylic acid (**30a**) and (*E*)-2 benzamido-3-(pyridin-4-yl)acrylic acid (**30b**) are shown in Figure 14. The isomer **30a** possesses a strong seven-membered ring intramolecular hydrogen bonding and shows quite different physicochemical properties, such as solubility and pKa, comparing with its isomer **30b**. The pconjugation between pyridyl and acrylate moieties is extended by intramolecular hydrogen bonding leading to a strong absorption at about 340 nm. Intramolecular proton transfer facilitates in the excited state, resulting in dual emission at around 420 nm and 490 nm in acetonitrile "(Guo et al., 2011)". Crystal structure of **30a** show a strong seven-membered ring intramolecular hydrogen bonding (Figure 15). The intramolecular proton transfer is facilitated by intramolecular hydrogen bond of O–H N. Tautomeric forms of **30a** is shown in Scheme 8.

N

O

O

P

O Ph

OMe

H

P N

O

EtO

Cl3C

O

H

**29II**

NH

O

**30b**

O

HO

N P

O

OEt

CCl3

O

EtO OEt

O

bond in N-H O=P is stable than that of in N-H O=C "(Corbridge, 1990)".

P

O

CCl3

Ph O

MeO

OEt

P O

O P

**29I**

EtO

H N

NH

O

**30a**

**Figure 14.** Formula structures of **30a** and **30b**.

O

OEt

H N

EtO

N

H

O

O

Cl3C

**Scheme 8.** Possible tautomeric forms of **30a**.

There is hydrogen bonding between the acrylate O(3) and the pyridine N(2) atoms; the distance between these two atoms is 2.483 Å, and the O(3)-H(12)-N(2) angle is 171.3°. The O(3)-H(12) distance is 1.345 Å (the theoretical distance is 0.920 Å for general carboxyl O-H bond), which is longer than the N(2)-H(12) distance of 1.145 Å (the general distance is 0.960 Å). The distance difference revealed that H(12) is closer to the pyridine N(2) than it is to the acrylate O(3). The O(2)-C(9) and O(3)-C(9) distances are 1.233 Å and 1.272 Å, respectively. These results show that H(12) is involved in a strong intramolecular hydrogen bonding. N(2)-H(12)····O(3), in which the H(12) interaction with the pyridine N(2) is stronger than that with O(3) atom. The carboxylic acid proton moves to the pyridine N atom, while an electron delocalizes across O(2), O(3), and C(9) to form two almost equivalent carbonyl groups. These results provide further evidence that compound **30a** exists mainly as a tautomeric form **30a** (NH) in the solid state (**30a[II]**) form "(Guo, et al. (2011)".

Resorcarene derivatives are used as units in self-assembled capsules via hydrogen bonds. Like to calixarenes, resorcarenes are the core to which specific functional groups are attached. These groups are responsible for the hydrogen bonds while the resorcarenes offer the right spatial arrangement of them. McGillivray and Atwood found that **31** forms in the crystalline state a hexameric capsule with the internal volume of about 1375Å3. There are 60 hydrogen bonds in hexameric with the help of eight molecules of water (Fig. 16) "(McGillivray & Atwood, 1997)".

**Figure 16.** Formula structure of **31** unit and crystal structure of **(31)6·8H2O**.

Yoshida et al. have also been reported the formation of a three-dimensional hydrogen bonding network by self-assembly of the Cu(II) complex of a semi-bidentate Schiff base "(Yoshida et al., 1997)". The crystal structure of the Cu(II) complex of Shiff base **32** is shown in Fig. 17. The infinite overall structure of **32** is found to be organized by a threedimensional hydrogen-bonding network in which the –NH2 O2S– type intermolecular hydrogen bonds play an important role, as shown in Fig. 18. One complex molecule is surrounded by four adjacent complexed molecules through four –NH2 O2S– hydrogen bonds. These hydrogen bonds would be strong judging from the NH O distances in the range 2.032–2.941 Å. From the neutron diffraction study of sulfamic acid (NH3+SO3- ), a comparably strong hydrogen bond has been observed (–N+H - O–S– distances in the range 1.95–2.56 Å) "(Jeffrey & Saenger, 1991)". Similar hydrogen bonds between sulfone and hydroxyl groups [2.898(6) Å] have been found in a supramolecular carpet formed *via* selfassembly of bis(4,4'-dihydroxyphenyl) sulfone "(Davies et al., 1997)". Furthermore, four weak Br H hydrogen bonds may participate in the hydrogen-bonding arrays "(Yoshida et al., 1997)".

Yang et al. reported the crystal structure of Bis(barbiturato)triwater complex of copper(II). The neutral Cu(H2O)3(barb)2 molecules are held together to form an extensive threedimensional network *via* –OH·····O– and –NH·····O– hydrogen-bonded contacts "(Yang et al., 2003)". Hydrogen bonding motifs in fullerene chemistry have been reported by Martín et al. as a minireviewe. The combination of fullerenes and hydrogen bonding motifs is a new interdisciplinary field in which weak intermolecular forces allow modulation of one-, two-, and three-dimensional fullerene-based architectures and control of their function "(Martín et al., 2005)".

**Figure 17.** Crystal structure of **32** unit.

208 Recent Advances in Crystallography

al., 1997)".

al., 2005)".

**Figure 16.** Formula structure of **31** unit and crystal structure of **(31)6·8H2O**.

comparably strong hydrogen bond has been observed (–N+H -

Yoshida et al. have also been reported the formation of a three-dimensional hydrogen bonding network by self-assembly of the Cu(II) complex of a semi-bidentate Schiff base "(Yoshida et al., 1997)". The crystal structure of the Cu(II) complex of Shiff base **32** is shown in Fig. 17. The infinite overall structure of **32** is found to be organized by a threedimensional hydrogen-bonding network in which the –NH2 O2S– type intermolecular hydrogen bonds play an important role, as shown in Fig. 18. One complex molecule is surrounded by four adjacent complexed molecules through four –NH2 O2S– hydrogen bonds. These hydrogen bonds would be strong judging from the NH O distances in the range 2.032–2.941 Å. From the neutron diffraction study of sulfamic acid (NH3+SO3-

1.95–2.56 Å) "(Jeffrey & Saenger, 1991)". Similar hydrogen bonds between sulfone and hydroxyl groups [2.898(6) Å] have been found in a supramolecular carpet formed *via* selfassembly of bis(4,4'-dihydroxyphenyl) sulfone "(Davies et al., 1997)". Furthermore, four weak Br H hydrogen bonds may participate in the hydrogen-bonding arrays "(Yoshida et

Yang et al. reported the crystal structure of Bis(barbiturato)triwater complex of copper(II). The neutral Cu(H2O)3(barb)2 molecules are held together to form an extensive threedimensional network *via* –OH·····O– and –NH·····O– hydrogen-bonded contacts "(Yang et al., 2003)". Hydrogen bonding motifs in fullerene chemistry have been reported by Martín et al. as a minireviewe. The combination of fullerenes and hydrogen bonding motifs is a new interdisciplinary field in which weak intermolecular forces allow modulation of one-, two-, and three-dimensional fullerene-based architectures and control of their function "(Martín et

), a

O–S– distances in the range

**Figure 18.** Crystal packing diagram of **32**.

Methyl 2,4-dimethoxy salicylate (**33**) as potential antitumor activity, was synthesized from the reaction of 1,3,5-trimethoxybenzene (the most electron-rich aromatic ring) with 2 methoxycarbonyl-5-(4-nitrophenoxy) tetrazole, under solvent-free conditions, a low yield product was obtained (< 2%), while in the presence of a Lewis acid (AlCl3), the yield was increased to 30% (a kind of trans esterification reaction) "(Dabbagh et al., 2003)".

Crystal structure of **33** is shown in Fig. 19. The carbon-oxygen framework of the molecular structure of **33** is essentially planar; bond lengths and angles are summarized in Table 6, while a structural diagram is shown also in Fig. 20. Planarity is maintained by a strong intramolecular hydrogen bonding interaction between the carbonyl-oxygen and phenolic-H

#### 210 Recent Advances in Crystallography

atom [H(1) O(1) = 1.68(4) Å; O(5) – H(1) = 1.00(4) Å], and a much weaker intramolecular hydrogen bond of distance 2.535 Å between Me hydrogen's [H(8)] and the C=O group (in what we label a "bisected" conformation with C*s* symmetry, Figs. 19 and 20). The orientations of the *o*-OMe and ester-OMe are such to minimize steric interactions. The structure of **33** was also calculated by semi-empirical *ab*-*initio*, *PM*3 and *AM*1 methods, and data for bond lengths, angles and torsion angles are in good agreement together with the experimental ones (Tables 6 and 7), while the corresponding calculated H(1) O(1) bond lengths were 1.57, 1.78 and 1.97 Å,

**Figure 19.** Crystal structure of **33** with 50% probability ellipsoids.

**Figure 20.** Diagrams showing the favored so-called "bisected" (left) and "eclipsed" (right) conformations of **33**.

and the calculated O(5) – H(1) values were 1.00, 0.980, 0.970 Å, respectively. The *ab-initio*  value for the weaker hydrogen bonding interaction was 2.574 Å. The *ab-initio* calculation also revealed a 1.40 Kcal higher energy, eclipsed conformation with C*1* symmetry (Fig. 21 c and d, Fig. 20, Table 7) with an H(8) – carbonyl bond length of 2.14 Å "(Dabbagh et al., 2004)".

**Figure 21.** Molecular structures for **33** from *ab-initio* analysis [side-view: **a** (bisected); **c** (eclipsed), and front-view: **b** (bisected0; **d** (eclipsed)].


a Atom numbering is as in Fig. 19.

210 Recent Advances in Crystallography

atom [H(1) O(1) = 1.68(4) Å; O(5) – H(1) = 1.00(4) Å], and a much weaker intramolecular hydrogen bond of distance 2.535 Å between Me hydrogen's [H(8)] and the C=O group (in what we label a "bisected" conformation with C*s* symmetry, Figs. 19 and 20). The orientations of the *o*-OMe and ester-OMe are such to minimize steric interactions. The structure of **33** was also calculated by semi-empirical *ab*-*initio*, *PM*3 and *AM*1 methods, and data for bond lengths, angles and torsion angles are in good agreement together with the experimental ones (Tables 6 and 7), while the corresponding calculated H(1) O(1) bond lengths were 1.57, 1.78 and 1.97 Å,

**Figure 19.** Crystal structure of **33** with 50% probability ellipsoids.

MeO

4

4

O

O

O

OMe

MeO

conformations of **33**.

H

O

5

1

OMe

3

**33**

23

5 6

H

H

**33A** (bisected) **33B** (eclipsed)

H

**Figure 20.** Diagrams showing the favored so-called "bisected" (left) and "eclipsed" (right)

O

1

2

H

8

H

O

OMe

H

O

<sup>H</sup> <sup>H</sup>

H

O

H

H

7

O

MeO

**Table 6.** Bond lengths (Å) and angles (o) of **33**.

#### 212 Recent Advances in Crystallography


aAverage of three calculations.

**Table 7.** Experimental and calculateda hydrogen bond lengths and energies (kcal/mol) for bisected and eclipsed structure of **33**.

**Figure 22.** Crystal packing diagram of **34** (a) and **35** (b). Intermolecular hydrogen bond assigned by red dashed line (Carbon: grey; hydrogen: white; oxygen: red and nitrogen: blue).

Tetrazole ring can exist to be an equilibrium mixture of two tautomeric forms (1*H* and 2*H*tetrazoles) "(Dabbagh & Lwowski, 2000)". 5-Aryloxy (1*H*) and/or (2*H*)-tetrazoles often show intermolecular hydrogen bond "(Noroozi Pesyan, 2011)". For instance, the crystal packing diagram of 5-(2,6-dimetylphenoxy)-(1*H*)-tetrazole (**34**) and 5-(2,6-diisopropylphenoxy)-(1*H*) tetrazole (**35**) show intermolecular hydrogen bond (Fig. 22). In the compound **34**, the crystal structure indicated that the tetrazole and phenyl rings are nearly perpendicular to each other, forming a dihedral angle of 95.5° (*versus* 92.06° from calcd. B3LYP/6-31G(d) and 6- 31+G(d)). Because of the conjugation of O1 with tetrazole ring, the bond distance C1–O1 [1.322 Å] is slightly shorter than O1–C7 [1.399 Å]. These bond distances for C1–O1 and O1– C2 were obtained 1.333 and 1.419 Å with calculation by B3LYP/6-31G(d) method, respectively and also 1.332 and 1.420 Å derived with calculation by B3LYP/6-31+G(d) basis set, respectively. These data are in good agreement with experimental results (Table 8). In the compound **35**, the crystal structure indicated that the tetrazole and phenyl rings are nearly perpendicular to each other, forming a dihedral angle of 85.91° (*versus* 107.2° from calcd. B3LYP/6-31G(d)). Because of the conjugation of O1 with tetrazole ring, the bond distance C2–O1 [1.3266(14) Å] is slightly shorter than O1–C7 [1.4257(13) Å]. These bond distances for C2–O1 and O1–C7 were obtained 1.332 and 1.423 Å with calculation by B3LYP/6-31+G(d) method, respectively and are in good agreement with experimental results. These bond distances were also obtained 1.322 and 1.422 Å with calculation by B3LYP/6-31G(d) method, respectively. The torsion angles between phenyl ring and each of methyl units on two isopropyl groups are -110.70°, 124.18° and 116.15° and 154.12°, respectively (Table 9).The selected parameters of bond length, angles and torsion angles of **34** and **35** derived by experimental and calculated results are shown in Tables 8 and 9.

212 Recent Advances in Crystallography

aAverage of three calculations.

eclipsed structure of **33**.

Bisected Eclipsed Relative

(kcal/mol) Å Å (kcal/mol) Å Å (Eeclip -Ebist)

**Table 7.** Experimental and calculateda hydrogen bond lengths and energies (kcal/mol) for bisected and

**Figure 22.** Crystal packing diagram of **34** (a) and **35** (b). Intermolecular hydrogen bond assigned by red

dashed line (Carbon: grey; hydrogen: white; oxygen: red and nitrogen: blue).

Method Etotal [C=O--H-C] [C=O--H-O] Etotal [C=O--H-C] [C=O--H-O]

X-Ray - 2.535 1.68(4) - - - - *Ab-intio* - 470792.80 2.574 1.565 -470791.40 2.139 1.557 1.40 PM3 -2812.50 2.647 1.780 -2811.10 2.309 1.780 1.40 AM1 -2813.50 2.554 1.974 -2812.50 2.186 1.969 1.0

Energy

The crystal packing of **34** exhibits an intermolecular N1–H1 N4 hydrogen bonds and comparized with the calculated at DFT (B3LYP) at 6-31G(d) and 6-31+G(d) basis sets (Table 10). The crystal structure indicated that the bond distance value between donor – hydrogen (N1–H1) and hydrogen-acceptor (H1 N4) were found in results 0.861 and 1.959 Å, respectively. For instance, these bond distances were also found in results 1.033 for (N1–H1) and 1.814 for (H1 N4) by calculated at B3LYP/6-31G(d) and 1.031 for (N1–H1) and 1.809 for (H1 N4) B3LYP/6-31+G(d), respectively. The donor-acceptor distance value (N1 N4) was obtained 2.804 by experimental method. This parameter was found 2.842 and 2.838 Å by calculated methods B3LYP/6-31G(d) and 6-31+G(d), respectively. The angle of N1-H1 N4 was found 169.9, 172.9 and 172.1° by experimental, calculated B3LYP/6-31G(d) and B3LYP/6-31+G(d) basis sets, respectively. The results of calculated method (specially 6- 31+G(d) basis set) are in good agreement with experimental results (Table 10).

The crystal packing of **35** also exhibits an intermolecular N3–H31 N6 hydrogen bonds and comparized with the calculated at DFT (B3LYP) at 6-31G(d) and 6-31+G(d) basis sets (Table 10). The crystal structure indicated that the bond distance value between donor – hydrogen (N3–H) and hydrogen-acceptor (H31 N6) were found in results 0.926 and 1.919 Å, respectively. For instance, these bond distances were also found in results 1.03 for (N3–H31) and 1.91 for (H31 N6) by calculated at B3LYP/6-31G(d) and 1.01 for (N3–H) and 1.93 for

#### 214 Recent Advances in Crystallography


a Calculated at B3LYP/6-31+G(d) basis set.

b Calculated at B3LYP/6-31G(d) basis set.

**Table 8.** The selected bond lengths (Å), angles (°) and torsion angles (φ) for **34**. Experimental and B3LYP/6-31+G(d) and B3LYP/6-31G(d).

(H N6) B3LYP/6-31+G(d), respectively. The donor-acceptor distance value (N3 N6) was obtained 2.835 by experimental method. This parameter was found 2.941 and 2.912 Å by calculated methods B3LYP/6-31G(d) and 6-31+G(d), respectively. The angle of N3–H31 N6 was found 169.1, 177.0 and 173.0° by experimental, calculated B3LYP/6-31G(d) and B3LYP/6-31+G(d) basis sets, respectively. The results of calculated method (specially 6- 31+G(d) basis set) are in good agreement with experimental results (Table 10). Compounds **34** (entry no. CCDC-838541) and **35** (entry no. CCDC-819010) were deposited to the Cambridge Crystallographic Data Center and are available free of charge upon request to CCDC, 12 Union Road, Cambridge, UK (Fax: +44-1223-336033, *e-mail*: *deposit@ccdc.cam.ac.uk*).


a Calculated at B3LYP/6-31+G(d) basis set.

b Calculated at B3LYP/6-31G(d) basis set.

214 Recent Advances in Crystallography

a Calculated at B3LYP/6-31+G(d) basis set. b Calculated at B3LYP/6-31G(d) basis set.

B3LYP/6-31+G(d) and B3LYP/6-31G(d).

Compd. **34**

Atom Ex. Calcd.a Calcd.b O1-C1 1.322 1.332 1.333 O1-C2 1.399 1.420 1.419 C1-N1 1.327 1.348 1.348 C1-N4 1.305 1.316 1.315 N1-N2 1.354 1.362 1.363 N1-H1 0.861 1.01 1.01 N2-N3 1.285 1.288 1.288 N3-N4 1.368 1.368 1.368 C2-C3 1.349 1.397 1.396 C2-C7 1.389 1.397 1.396 C3-C9 1.518 1.508 1.508 C7-C8 1.495 1.508 1.508 C1-O1-C2 117.3 117.6 117.6 O1-C1-N1 121.0 120.8 120.8 O1-C1-N4 129.3 130.05 130.05 C1-N1-H1 126.1 130.4 130.4 O1-C2-C3 117.8 117.8 117.8 O1-C2-C7 116.3 117.8 117.8 C2-C3-C9 120.4 121.2 121.2 C2-C7-C8 123.0 121.2 121.2 C2-O1-C1-N1 170.0 -180 -180 O1-C1-N1-H1 -0.8 0.0 0.0 O1-C2-C3-C9 4.4 4.9 4.9 O1-C2-C3-C4 -175.4 -175.6 -175.6 O1-C2-C7-C8 -5.7 -4.9 -4.9

**Table 8.** The selected bond lengths (Å), angles (°) and torsion angles (φ) for **34**. Experimental and

(H N6) B3LYP/6-31+G(d), respectively. The donor-acceptor distance value (N3 N6) was obtained 2.835 by experimental method. This parameter was found 2.941 and 2.912 Å by calculated methods B3LYP/6-31G(d) and 6-31+G(d), respectively. The angle of N3–H31 N6 was found 169.1, 177.0 and 173.0° by experimental, calculated B3LYP/6-31G(d) and B3LYP/6-31+G(d) basis sets, respectively. The results of calculated method (specially 6- 31+G(d) basis set) are in good agreement with experimental results (Table 10). Compounds **34** (entry no. CCDC-838541) and **35** (entry no. CCDC-819010) were deposited to the Cambridge Crystallographic Data Center and are available free of charge upon request to CCDC, 12 Union Road, Cambridge, UK (Fax: +44-1223-336033, *e-mail*: *deposit@ccdc.cam.ac.uk*).

**Table 9.** The selected bond lengths (Å), angles (°) and torsion angles (φ) for **35**. Experimental and B3LYP/6-31+G(d) and B3LYP/6-31G(d).

#### 216 Recent Advances in Crystallography


a Experimental.

b Symmetry codes: (i) *x*, −*y*+3/2, *z*+1/2.

c Calculated at B3LYP/6-31G(d).

d Calculated at B3LYP/6-31+G(d).

e Symmetry codes: (i) *x*, −*y*+3/2, *z*+1/2.

**Table 10.** Experimental and calculated B3LYP/6-31+G(d) and B3LYP/6-31G(d) levels for hydrogen-bond geometry of **34** and **35** (Å, °)

**Figure 23.** Formula and crystal structures of the compounds **36a** and **36b**.

Nickel(II) complexes containing specific phosphorus– oxygen chelating ligands are very efficient catalysts for the oligomerisation of ethylene to linear form "(Braunstein et al., 1994)". For instance, Nickel(II) diphenylphosphinoenolate complexes have been prepared from (*ortho-* HX- substituted benzoylmethylene)triphenyl phosphoranes (X = NMe, NPh) and [Ni(1,5-cod)2] in the presence of a tertiary phosphine (PPh3 or P(*p*-C6H4F)3) and their crystal structures have been studied by Braunstein et al. (structures of **36a** and **36b**). Formula and crystal structures of the compounds **36a** and **36b** are shown in Fig. 23. Crystallographic study of the complexes **36a**  and **36b** establishes the presence of strong intramolecular hydrogen bonding between the enolate oxygen and the N–H functional group "(Braunstein et al., 2005)". The most notable feature in these structures is the strong intramolecular N–H····O hydrogen bonding: the calculated distance between the NH hydrogen atom and the oxygen atom of the enolate ligand is short: 2.18(5) Å in **36a** and 2.00(5) Å in **36b**, respectively "(Taylor & Kennard, 1982)".

216 Recent Advances in Crystallography

b Symmetry codes: (i) *x*, −*y*+3/2, *z*+1/2.

Symmetry codes: (i) *x*, −*y*+3/2, *z*+1/2.

 Calculated at B3LYP/6-31G(d). d Calculated at B3LYP/6-31+G(d).

geometry of **34** and **35** (Å, °)

Calcd.c

Calcd.c

c

e

a Experimental.

D-H A D-H H A D A D-H A (degree, °)

Exp.a (**34**) N1-H1 N4b 0.861 1.959 2.804 166.9

**Figure 23.** Formula and crystal structures of the compounds **36a** and **36b**.

Nickel(II) complexes containing specific phosphorus– oxygen chelating ligands are very efficient catalysts for the oligomerisation of ethylene to linear form "(Braunstein et al., 1994)". For instance, Nickel(II) diphenylphosphinoenolate complexes have been prepared from (*ortho-*

 (**34**) 1.033 1.814 2.842 172.9 Calcd.d (**34**) 1.031 1.809 2.838 172.1 Exp.a (**35**) N3-H31 N6e 0.926 1.919 2.835 169.1

 (**35**) 1.03 1.91 2.941 177 Calcd.d (**35**) 1.01 1.93 2.912 174

**Table 10.** Experimental and calculated B3LYP/6-31+G(d) and B3LYP/6-31G(d) levels for hydrogen-bond

Intramolecular hydrogen bond is also shown in alkoxyamines. These compounds and persistent nitroxide radicals are important regulators of nitroxide mediated radical polymerization (NMP). The formula and crystal structure of β-phosphorylated nitroxide radical (**37**) is shown in Fig. 24. Compound **37** show an eight-membered intramolecular hydrogen bond between P=O····H-O (versus N-O····H-O). The hydrogen bond distance for two enantiomers of **37** is different. The hydrogen bond distances of P=O····H-O in (*R*)- and (*S*)-**37** are 1.570 and 2.040 Å, respectively and favored. Instead, the hydrogen bond distance for N-O····H-O in (*R*)- and (*S*)-**37** are 3.070 and 3.000 Å, respectively and unfavored "(Acerbis et al., 2006)".

**Figure 24.** Formula and crystal structure of two enantiomers of compound **37** (O: red, N: blue and P: yellow).

1,8-diaminonaphthalene derivatives such as; *N*-(8-(dimethylamino)naphthalen-1-yl)-2 fluoro-*N*-methylbenzamide (**38**) is a proton sponge. An unusual strong intramolecular hydrogen bond was observed in the protonated **38**. In compound **38** in which a protonated amine group (**38-H+**) can act as a donor suitably positioned to engage in a strong intramolecular hydrogen bond with the amide nitrogen atom rather than with the carbonyl oxygen atom (Scheme 9). Crystal structure of the triflate salt of **38-H+** is shown in Fig. 25. The unit cell consists of two molecules of **38-H+**, two triflate counter ions, and one molecule of water. The dashed line indicates the proposed hydrogen bond between H1A and N2A. Selected bond lengths and angles are N2A–H1A = 2.17(4), N1A–N2A = 2.869(5), C14A–N2A = 1.369(5) (Å) and N2A–H1A–N1A = 136(3)° "(Cox et al., 1999)".

**Scheme 9.** Protonation of **38** in the presence of trifluoromethanesulfonic acid (TfOH).

**Figure 25.** Crystal structure of the triflate salt of **38-H+** (50% ellipsoids and triflate counter ion is omitted).

2,4,6-Trisubstituted phenolic compounds such as 2,4,6-tri-*tert*-butyl phenol are as antioxidant "(Jeong et al., 2004)". Owing to the nature of the catalytic centres of galactose oxidase (GAO) and glyoxal oxidase (GLO), the *N*,*O*-bidentate pro-ligand, 2'-(4',6'-di-*tert*butylhydroxyphenyl)-4,5-diphenyl imidazole (LH) (**39**) has been synthesized "(Benisvy et al., 2001)". The compound **39** possesses no readily oxidisable position (other than the phenol) and involves *o*- and *p*-substituents on the phenol ring that prevent radical coupling reactions. The compound **39** undergoes a reversible one-electron oxidation to generate the corresponding [LH]·+ radical cation that possesses phenoxyl radical character. The unusual reversibility of the [LH]/[LH]·+ redox couple is attributed to a stabilisation of [LH]·+ by intramolecular O–H N hydrogen bonding "(Benisvy et al., 2003)". The formula and crystal structure of **39** are shown in Fig. 26. Crystal structure of **39** shows an intra- and intermolecular hydrogen bonds in **39**. In respect of the chemical properties of **39**, there is a strong intramolecular hydrogen bond between the phenolic O–H group and N(5) of imidazole ring. The strength of this hydrogen bond, as measured by the O(1) N(5) distance of 2.596(2) Å and the O(1)–H(1) N(5) angle of 150.7°. Also, the N–H group of imidazole ring in **39** is involved in an intermolecular N–H O hydrogen bond [N(2) O(1S) 2.852(2) Å and N(2)–H(2A) O(1S) 168.8°] to an adjacent trapped acetone molecule (**39·Me2CO**) "(Benisvy et al., 2003)".

**Figure 26.** Formula and crystal structure of **39·Me2CO**.

218 Recent Advances in Crystallography

1,8-diaminonaphthalene derivatives such as; *N*-(8-(dimethylamino)naphthalen-1-yl)-2 fluoro-*N*-methylbenzamide (**38**) is a proton sponge. An unusual strong intramolecular hydrogen bond was observed in the protonated **38**. In compound **38** in which a protonated amine group (**38-H+**) can act as a donor suitably positioned to engage in a strong intramolecular hydrogen bond with the amide nitrogen atom rather than with the carbonyl oxygen atom (Scheme 9). Crystal structure of the triflate salt of **38-H+** is shown in Fig. 25. The unit cell consists of two molecules of **38-H+**, two triflate counter ions, and one molecule of water. The dashed line indicates the proposed hydrogen bond between H1A and N2A. Selected bond lengths and angles are N2A–H1A = 2.17(4), N1A–N2A = 2.869(5), C14A–N2A

**38 38-H<sup>+</sup>**

**Figure 25.** Crystal structure of the triflate salt of **38-H+** (50% ellipsoids and triflate counter ion is omitted).

2,4,6-Trisubstituted phenolic compounds such as 2,4,6-tri-*tert*-butyl phenol are as antioxidant "(Jeong et al., 2004)". Owing to the nature of the catalytic centres of galactose oxidase (GAO) and glyoxal oxidase (GLO), the *N*,*O*-bidentate pro-ligand, 2'-(4',6'-di-*tert*butylhydroxyphenyl)-4,5-diphenyl imidazole (LH) (**39**) has been synthesized "(Benisvy et al., 2001)". The compound **39** possesses no readily oxidisable position (other than the phenol) and involves *o*- and *p*-substituents on the phenol ring that prevent radical coupling reactions. The compound **39** undergoes a reversible one-electron oxidation to generate the

**Scheme 9.** Protonation of **38** in the presence of trifluoromethanesulfonic acid (TfOH).

N N

<sup>O</sup> Me <sup>F</sup> <sup>H</sup>

<sup>2</sup> <sup>1</sup> HOTf

Me Me

OTf

= 1.369(5) (Å) and N2A–H1A–N1A = 136(3)° "(Cox et al., 1999)".

Me Me

N N

<sup>O</sup> Me <sup>F</sup>

The azamacrocyclic ligand 1,4,7-triazacyclononane or TACN, **40**, has attracted considerable interest in recent years for its applications in oxidative catalysis. Another application of this compound was discussed by Pulacchini, et al. "(Pulacchini et al., 2003)". The incorporation of the 1,2-diaminocyclohexane moiety into a 1,4,7-triazacyclononane macrocyclic ligand was done by this research group, as it is an inexpensive starting material and both enantiomers are readily available. Moreover, this chiral framework has been included in a number of ligands that have been successfully applied in a range of asymmetric catalytic processes by Jacobsen et al. in metallosalen complexes "(Jacobsen & Wu, 1999)".

Crystal structure of **41** is shown in Fig. 27 and revealed the structure of the macrocyclic ligand in which the six-membered ring has chair conformation (Fig. 27). The asymmetric unit is completed by the two chloride ions and a water molecule in which all C–C, C–O and C–N bonds are unexceptional. Two short hydrogen bonding interactions of 2.724(4) Å between N(1)–H(01) O(1) and 2.884(5) between N(2)–H(05) O(1) within the macrocycle are then supplemented by an extensive hydrogen bonding network between the ammonium nitrogen atoms N(1) and N(2) the two chloride ions Cl(1) and Cl(2), as well as the water molecule of crystallisation, as shown in Fig. 28. The roles of the two chloride ions in the network are distinct with Cl(1) acting as a direct bridge between two macrocyclic moieties as well as linking to a third *via* a water molecule. In contrast, the second chloride ion, appears to essentially serve to template the macrocyclic ligand into the conformation observed *via* hydrogen bonding interactions with N(1)–H(01) and N(2)–H(05). The second chloride ion also links to other macrocyclic moieties *via* the water molecules.

The following hydrogen bond lengths (Å) were observed from the polymeric hydrogen bonding array in **41·2HCl·H2O**.; N(1)–H(06) Cl(1) 3.099(4), N(1)–H(01) Cl(2) 3.185(4), N(1)–H(01) N(2) 3.043(5), N(1)–H(01) O(1) 2.724(4), N(2)–H(02) Cl(1)#1 3.103(4), N(2)–H(05) Cl(2) 3.108(3), N(2)–H(05) O(1) 2.884(5), O(2)– H(04) Cl(1) 3.271(4), O(2)– H(03) Cl(2)#2 3.217(4) "(Pulacchini, (2003)".

**Figure 27.** Formula structures of **40** and **41** and crystal structure of **41·2HCl·H2O**.

**Figure 28.** Polymeric hydrogen bonding network in **41·2HCl·H2O** "(Pulacchini, (2003)".

220 Recent Advances in Crystallography

done by this research group, as it is an inexpensive starting material and both enantiomers are readily available. Moreover, this chiral framework has been included in a number of ligands that have been successfully applied in a range of asymmetric catalytic processes by

Crystal structure of **41** is shown in Fig. 27 and revealed the structure of the macrocyclic ligand in which the six-membered ring has chair conformation (Fig. 27). The asymmetric unit is completed by the two chloride ions and a water molecule in which all C–C, C–O and C–N bonds are unexceptional. Two short hydrogen bonding interactions of 2.724(4) Å between N(1)–H(01) O(1) and 2.884(5) between N(2)–H(05) O(1) within the macrocycle are then supplemented by an extensive hydrogen bonding network between the ammonium nitrogen atoms N(1) and N(2) the two chloride ions Cl(1) and Cl(2), as well as the water molecule of crystallisation, as shown in Fig. 28. The roles of the two chloride ions in the network are distinct with Cl(1) acting as a direct bridge between two macrocyclic moieties as well as linking to a third *via* a water molecule. In contrast, the second chloride ion, appears to essentially serve to template the macrocyclic ligand into the conformation observed *via* hydrogen bonding interactions with N(1)–H(01) and N(2)–H(05). The second

The following hydrogen bond lengths (Å) were observed from the polymeric hydrogen bonding array in **41·2HCl·H2O**.; N(1)–H(06) Cl(1) 3.099(4), N(1)–H(01) Cl(2) 3.185(4), N(1)–H(01) N(2) 3.043(5), N(1)–H(01) O(1) 2.724(4), N(2)–H(02) Cl(1)#1 3.103(4), N(2)–H(05) Cl(2) 3.108(3), N(2)–H(05) O(1) 2.884(5), O(2)– H(04) Cl(1) 3.271(4), O(2)–

Jacobsen et al. in metallosalen complexes "(Jacobsen & Wu, 1999)".

chloride ion also links to other macrocyclic moieties *via* the water molecules.

**Figure 27.** Formula structures of **40** and **41** and crystal structure of **41·2HCl·H2O**.

H(03) Cl(2)#2 3.217(4) "(Pulacchini, (2003)".

In all thiohelicene crystals (see also Figs. 1 and 2) specific interactions were found involving sulfur "(Nakagawa et al., 1985; Yamada et al., 1981)" and hydrogen atoms at distances slightly shorter than the sum of van der Waals radii (1.80 Å for S and 1.20 Å for H). They are quite probably attractive, and, in all structures except **TH11** (hexathia-[11] helicene **3**) they involve only atoms of terminal rings. In the case of the 5-ring system each molecule has two equivalent S S interactions of 3.544 Å, while each **TH7** (tetrathia-[7] helicene **1**) molecule is involved in four equivalent S H contacts measuring 2.89 Å. All these interactions occur between enantiomeric pairs. Crystal structyre of pentathia-[9] helicene (**TH9**, **42**) and crystal packing diagram of this compound including S H contacts are shown in Figs. 29 and 30, respectively. For **42**, each molecule presents four equivalent S H contacts at 2.87 Å, all with homochiral molecules giving rise to a quasihexagonal packing of tilted helices in planes parallel to the *ab* lattice plane. The crystal structure of **TH11** (**3**) is unusual because the asymmetric unit is formed by two complete molecules as opposed to half a molecule in all the lower racemic thiohelicenes. The packing environment of each of the two closely similar but crystallographically independent molecules, and of each of its halves, is unique: thus the *C*2 axes bisecting the central ring of each **TH11** (**3**) molecule are noncrystallographic. This situation is likely to arise in order to optimize the complex network of specific interactions involving S and H atoms. It leads to larger than expected asymmetric units and lower crystal symmetry, common occurrences in hydrogen bonded molecular systems. In the triclinic **TH11** (**3**) crystals four nonequivalent short S S and an equal number of S H interactions are found "(Caronna et al., 2001)". The essential geometric features of all these contacts in the racemic thiohelicene series and evidencing a remarkable consistency of the S H interaction with expectations for weak hydrogen bonds have been reported "(Desiraju & Steiner, 2000)".

**Figure 29.** Crystal structure of **TH9** (**42**).

**Figure 30.** Crystal packing diagram of **42** in which each molecule consists of four equivalent S····H contacts.

The fused pyrimidines such as pyrimido[4,5-*c*]pyridazine-5,7(6*H*,8*H*)-diones, which are common sources for the development of new potential therapeutic agents, is well known "(Altomare et al., 1998; Brown, 1984; Hamilton, 1971)". Some of this class of compounds play new heterocyclizations based on <sup>H</sup> NS methodology as *N*(2)-oxide and 3-alkylamino derivatives of 6,8-dimethylpyrimido[4,5-*c*]pyridazine-5,7(6*H*,8*H*)-dione "(Gulevskaya et al., 2003)".

Recently, the synthesis of 3-arylpyrimido[4,5-c]pyridazine-5,7(6*H*,8*H*)-diones (**43a–d**) and their sulfur analogs 3-aryl-7-thioxo-7,8-dihydropyrimido[4,5-c]pyridazin-5(6H)-ones **44a–d** have been reported "(Rimaz et al., 2010)". One of the most interesting intermolecular hydrogen bond in **43a–d** have been reported by our research group "(Rimaz et al., 2010)" (Figure 31). Owing to the less solubility of **43a–d** and **44a–d**, an attempt to achieve the single crystal of these compounds for investigation of the clustered water in their crystalline structure was failed. The 1H NMR spectra of **43a–d** show two broad singlets in the range of *δ* = 7.00–8.00 ppm that correspond to the protons of clustered water molecule in the **43a-d**. The chemical shift values of two variable protons of water in **43a–d** in ambient temperature are shown in Table 11. There are some reasons for demonstration and interpretation of this criterion. (i) One of the evidence is the mass spectra. The mass spectra of the compounds **43a–d** show not only the molecular ion fragment (M) but also the fragment of M+18. Therefore, the strength of hydrogen bond between the proton of H2O (Ha) and oxygen atom of carbonyl group (C5=O Ha–O) and also hydrogen bond between the N6–H of **43a–d** and oxygen atom of H2O (N6–H O–Ha) is considered more than that of the hydrogen bonding in the dimer form of **43a–d**  (judging by the observation of the M+18 ion) (Fig. 32) "(Rimaz et al., 2010)". It seems that at least one molecule of water clustered and joined to **43** and **44** by two strong intermolecular hydrogen bonds and dissociated neither by DMSO molecules as a polar aprotic solvent nor in mass ionization chamber. Presumably, this intermolecular hydrogen bond is of quasi-covalent hydrogen bond type. There are some reports on literatures about quasi-covalent hydrogen bonds "(Dabbagh et al., 2007; Gilli et al., 1994, 2000, 2004; G. Gilli & P. Gilli, 2000; Golič et al., 1971; Madsen et al., 1999; Nelson, 2002; Steiner, 2002; Vishweshwar et al., 2004; Wilson, 2000)".

**Figure 31.** Formula structures of **43a–d·(H2O)** and **44a–d·(H2O)**.

222 Recent Advances in Crystallography

**Figure 29.** Crystal structure of **TH9** (**42**).

play new heterocyclizations based on <sup>H</sup>

contacts.

2003)".

**Figure 30.** Crystal packing diagram of **42** in which each molecule consists of four equivalent S····H

The fused pyrimidines such as pyrimido[4,5-*c*]pyridazine-5,7(6*H*,8*H*)-diones, which are common sources for the development of new potential therapeutic agents, is well known "(Altomare et al., 1998; Brown, 1984; Hamilton, 1971)". Some of this class of compounds

derivatives of 6,8-dimethylpyrimido[4,5-*c*]pyridazine-5,7(6*H*,8*H*)-dione "(Gulevskaya et al.,

Recently, the synthesis of 3-arylpyrimido[4,5-c]pyridazine-5,7(6*H*,8*H*)-diones (**43a–d**) and their sulfur analogs 3-aryl-7-thioxo-7,8-dihydropyrimido[4,5-c]pyridazin-5(6H)-ones **44a–d** have

NS methodology as *N*(2)-oxide and 3-alkylamino

**Figure 32.** Representatively, strong intermolecular hydrogen bond and the chemical shifts of two hydrogen bonded protons of clustered water molecule with **43a** "(Rimaz et al., 2010)".


a Two protons of water are equivalent in chemical shift appeared up-fielded as a broad singlet in **44a–d**.

**Table 11.** The chemical shift values of the two protons of a clustered water molecule in **43a–d** and **44a– d**a at ambient temperature "(Rimaz et al., 2010)".

The proton/deuterium exchange was examined on **43a–d** by adding one drop of D2O. Interestingly, from hydrogen to fluorine substituent on phenyl ring in **43a–d** the exchange rate was decreased, and no deuterium exchanging of Ha and Hb was observed in **43d** while the amide protons were easily exchanged (Fig. 33). This phenomenon attributed to the fluorine atom that has made new intermolecular hydrogen bond with Ha and Hb of clustered water molecule in another molecule of **43d**. The intermolecular hydrogen bond of fluorine with the proton of clustered water (–F····Ha– and –F····Hb–) in **43d** inhibited the proton/deuterium exchanging of the clustered water protons. However, the electronegativity of fluorine atom caused deshielding of Ha and Hb on **43d** and blocked the proton/deuterium exchange (Fig. 33 and Scheme 10). Two conformational forms of **IA** and **IB** in **43d** are equivalent because of free rotation of phenyl ring about the C3–C9 and C12–F single bonds (Scheme 10) "(Rimaz et al., 2010)".

### **2.3. Crystal structure of some organic spiro compounds**

Spiro compounds are very important and useful compounds and versatile applications. Many of heterocyclic spirobarbituric acids "(Kotha et al., 2005)", furo[2,3-*d*]pyrimidines "(Campaigne et al., 1969)" and fused uracils "(Katritzky & Rees, 1997; Naya et al., 2003)" are well known for their pharmaceutical and biological effects.

Recently, we have reported new spiro compound based on barbiturates; 5-alkyl and/or 5-aryl-1*H,* 1'*H*-spiro[furo[2,3-*d*]pyrimidine-6,5'-pyrimidine]2,2',4,4',6'*(*3*H,* 3'*H,* 5*H)*-pentaones which are dimeric forms of barbiturate (uracil and thiouracil derivatives) "(Jalilzadeh et al., 2011)". Reaction of 1,3-dimethyl barbituric acid (DMBA) with cyanogen bromide (BrCN) and acetaldehyde in the presence of triethylamine afforded 1,1',3,3',5-pentamethyl-1*H*,1'*H*spiro[furo[2,3-*d*]pyrimidine-6,5'-pyrimidine]-2,2',4,4',6'(3*H*,3'*H*,5*H*)-pentaone (**46**) in excellent yield "(Jalilzadeh et al., 2011)". The formula structures of spiro compounds derived from barbituric acid (BA, **45**), DMBA **46** and 1,3-thiobarbituric acid (TBA, **47**) is shown in Fig. 34. Attempt for single crystallization of spiro compounds **45** and **47** were unsuccessful. The crystal structure and crystal packing diagram of **46** are shown in Figs. 35 and 36. This compound was crystalized in triclinic system. Selected crystallographic data for **46** is summarized at Table 12.

224 Recent Advances in Crystallography

Compd. *δ* (ppm)

**44a** 4.89 **44b** 4.90 **44c** 4.90 **44d** 4.89

**d**a at ambient temperature "(Rimaz et al., 2010)".

**43a** 7.76 7.57 **43b** 7.75 7.61 **43c** 7.74 7.61 **43d** 7.75 7.61

a Two protons of water are equivalent in chemical shift appeared up-fielded as a broad singlet in **44a–d**.

about the C3–C9 and C12–F single bonds (Scheme 10) "(Rimaz et al., 2010)".

**2.3. Crystal structure of some organic spiro compounds** 

well known for their pharmaceutical and biological effects.

**Table 11.** The chemical shift values of the two protons of a clustered water molecule in **43a–d** and **44a–**

The proton/deuterium exchange was examined on **43a–d** by adding one drop of D2O. Interestingly, from hydrogen to fluorine substituent on phenyl ring in **43a–d** the exchange rate was decreased, and no deuterium exchanging of Ha and Hb was observed in **43d** while the amide protons were easily exchanged (Fig. 33). This phenomenon attributed to the fluorine atom that has made new intermolecular hydrogen bond with Ha and Hb of clustered water molecule in another molecule of **43d**. The intermolecular hydrogen bond of fluorine with the proton of clustered water (–F····Ha– and –F····Hb–) in **43d** inhibited the proton/deuterium exchanging of the clustered water protons. However, the electronegativity of fluorine atom caused deshielding of Ha and Hb on **43d** and blocked the proton/deuterium exchange (Fig. 33 and Scheme 10). Two conformational forms of **IA** and **IB** in **43d** are equivalent because of free rotation of phenyl ring

Spiro compounds are very important and useful compounds and versatile applications. Many of heterocyclic spirobarbituric acids "(Kotha et al., 2005)", furo[2,3-*d*]pyrimidines "(Campaigne et al., 1969)" and fused uracils "(Katritzky & Rees, 1997; Naya et al., 2003)" are

Recently, we have reported new spiro compound based on barbiturates; 5-alkyl and/or 5-aryl-1*H,* 1'*H*-spiro[furo[2,3-*d*]pyrimidine-6,5'-pyrimidine]2,2',4,4',6'*(*3*H,* 3'*H,* 5*H)*-pentaones which are dimeric forms of barbiturate (uracil and thiouracil derivatives) "(Jalilzadeh et al., 2011)". Reaction of 1,3-dimethyl barbituric acid (DMBA) with cyanogen bromide (BrCN) and acetaldehyde in the presence of triethylamine afforded 1,1',3,3',5-pentamethyl-1*H*,1'*H*spiro[furo[2,3-*d*]pyrimidine-6,5'-pyrimidine]-2,2',4,4',6'(3*H*,3'*H*,5*H*)-pentaone (**46**) in excellent yield "(Jalilzadeh et al., 2011)". The formula structures of spiro compounds derived from barbituric acid (BA, **45**), DMBA **46** and 1,3-thiobarbituric acid (TBA, **47**) is shown in Fig. 34. Attempt for single crystallization of spiro compounds **45** and **47** were unsuccessful. The crystal structure and crystal packing diagram of **46** are shown in Figs. 35 and 36. This compound was crystalized in triclinic system. Selected crystallographic data for **46** is summarized at Table 12.

Ha Hb

**Figure 33.** Proton/deuterium exchangeability of the Ha and Hb of clustered H2O molecule in 1H NMR spectra of **43a** (A), **43b** (B), **43c** (C) and **43d** (D). The assigned spectra are shown before (a) and after added D2O (b). No exchange occurred in **43d** of clustered H2O protons (D) "(Rimaz et al., 2010)".

**Scheme 10.** Possible various types of intermolecular hydrogen bond of fluorine with a proton of a clustered were (-F····Hb- and -F····Ha-) in **43d**. This phenomenon presumably inhibited the proton/deuterium exchangeability of the clustered water protons.

**Figure 34.** Formula structures of **45-47**.

**Figure 35.** Crystal structure of **46.** 

226 Recent Advances in Crystallography

F

F

**Figure 34.** Formula structures of **45-47**.

N N

<sup>1</sup> <sup>2</sup> <sup>3</sup> <sup>4</sup> <sup>5</sup> <sup>6</sup> <sup>7</sup> <sup>8</sup>

N N

<sup>1</sup> <sup>2</sup> <sup>3</sup> <sup>4</sup> <sup>5</sup> <sup>6</sup> <sup>7</sup> <sup>8</sup>

proton/deuterium exchangeability of the clustered water protons.

9 10 11 12

9 10 11 12

N

Ha O Hb

F

N

Ha O Hb

F

clustered were (-F····Hb- and -F····Ha-) in **43d**. This phenomenon presumably inhibited the

O

H

N O H

O

H

F

F

**I(B)**

**Scheme 10.** Possible various types of intermolecular hydrogen bond of fluorine with a proton of a

**I(A)**

N N

N N

N

N

O H Ha O Hb

O

N

H

O H

Ha O Hb O

N

H

N O H

**Figure 36.** Crystal packing diagram of **46.**


**Table 12.** Selected crystallographic data for **46**.

Another spiro barbiturate compound derived from the reaction of DMBA with BrCN and acetone in the presence of triethylamine is 1,1',3,3',5,5'-Hexamethylspiro[furo-[2,3 *d*]pyrimidine-6(5*H*),5'-pyrimidine]-2,2',4,4',6'(1*H*,3*H*,1'*H*,3'*H*,5*H*)-pentaone (**48**) "(Noroozi Pesyan et al., 2009)". Reaction of aldehydes with (thio)barbiturates is faster than ketones due to the reactivity and less hindrance in aldehydes. The formula and crystal structure of **48** is shown in Figs. 37 and 38, respectively. In Fig. 38, the fused 2,3-dihydrofurane ring has an envaloped conformation, and spiro pyrimidine ring has a half-chair conformation. Spiro pyrimidine ring is nearly perpendicular to 2,3-dihydro furan ring moiety as was observed earlier in the related compound. Torsion angles C2-C1-O4-C7 and C2-C1-C5-C6 are - 99.39(3)° and 94.87(3) °, respectively. In the crystal, short intermolecular interaction O C contacts between the carbonyl groups prove an existing of electrostatic interactions, which link the molecules into corrugated sheets parallel to *ab* plane (Table 13).


Symmetry codes: (i) -x + 1, y -1/2, -z +3/2; (ii) x+1, y, z

**Table 13.** Selected interatomic distances (Å) in **48**.

**Figure 37.** Formula structure of **48**.

228 Recent Advances in Crystallography

*Crystal data*

Emprical formula C14H16N4O6 *M* 336.30 *T* 298 K *a* (Å) 8.974 (5) *b* (Å) 9.539 (5) *c* (Å) 10.314 (5) *α* ( ◦) 64.782 (5) *β* ( ◦) 69.349 (5) *γ* ( ◦) 69.349 (5) *V* (Å3*)* 725.8 (7)

*Z* 2 *F*(000) 352 *Dx* (mg m−3*)* 1.539 *λ* (Å) 0.71073 *μ*(mm−1*)* 0.12

*R*int 0.062 *θ*max 29.0 ◦ *θ*min 2.3 ◦

*R*[*F*2 *>* 2*σ(F*2*)*] 0.067 *wR*(*F*2*)* 0.203 *S* 1.04

Another spiro barbiturate compound derived from the reaction of DMBA with BrCN and acetone in the presence of triethylamine is 1,1',3,3',5,5'-Hexamethylspiro[furo-[2,3 *d*]pyrimidine-6(5*H*),5'-pyrimidine]-2,2',4,4',6'(1*H*,3*H*,1'*H*,3'*H*,5*H*)-pentaone (**48**) "(Noroozi Pesyan et al., 2009)". Reaction of aldehydes with (thio)barbiturates is faster than ketones due to the reactivity and less hindrance in aldehydes. The formula and crystal structure of **48** is shown in Figs. 37 and 38, respectively. In Fig. 38, the fused 2,3-dihydrofurane ring has an envaloped conformation, and spiro pyrimidine ring has a half-chair conformation. Spiro pyrimidine ring is nearly perpendicular to 2,3-dihydro furan ring moiety as was observed earlier in the related compound. Torsion angles C2-C1-O4-C7 and C2-C1-C5-C6 are - 99.39(3)° and 94.87(3) °, respectively. In the crystal, short intermolecular interaction O C contacts between the carbonyl groups prove an existing of electrostatic interactions, which

C8 O2<sup>i</sup> 2.835 (4) C3 O5ii 2.868 (4)

*Data collection*

*Refinement*

link the molecules into corrugated sheets parallel to *ab* plane (Table 13).

**Table 12.** Selected crystallographic data for **46**.

Symmetry codes: (i) -x + 1, y -1/2, -z +3/2; (ii) x+1, y, z **Table 13.** Selected interatomic distances (Å) in **48**.

**Figure 38.** Crystal structure of **48**.

One of another interesting spiro barbiturate compound is the trimeric form of 1,3- DMBA; 5,6-dihydro - 1,3-dimethyl - 5,6 – bis - [l',3'-dimethyl-2',4',6'-trioxo-pyrimid(5',5')yl]furo[2,3 *d*]uracil (**49**). This compound was first reported by electrochemical method "(Kato et al., 1974; Kato & Dryhurst, 1975; Poling & van der Helm, 1976)" and it has been reported the synthesis of **49** by chemical method for a first time two years ago "(Hosseini et al., 2011)". The formula and crystal structures of **49** are shown in Figs. 39 and 40, respectively. Crystals of **49** were obtained by slow evaporation of a solution of **49** in acetone at room temperature. The data were acquired using a STOE IPDS II diffractometer, data collection and cell refinement were processed using STOE X-AREA "(Stoe & Cie, 2002)" and data reduction was processed using STOE X-RED "(Stoe & Cie, 2002)" program. Program(s) used to refine structure was *SHELXL97* "(Sheldrick, 1997). Crystal data for **49**: Orthorhombic; C18H18N6O9; M = 462.38; Unit cell parameters at 293(2) K: *a* = 13.2422(4), *b* = 15.9176(6), *c* = 19.5817(6) Å; α = β = γ = 90*°*; V = 4127.5(2) Å3; *Z* = 8; μ = 0.122 mm–1; Total reflection number 4275; 304 parameters; λ = 0.71073 Å; 2916 reflections with *I* > 2σ(*I*); Rint = 0.056; *θ*max = 26.49°; *R*[*F*2 > 2 σ(*F*2)] = 0.048; *wR*(*F*2) = 0.112; *S* = 1.02, F000 = 1920 "(Hosseini et al., 2011)".

**Figure 39.** Formula structure of **49**.

**Figure 40.** Crystal structure of **49**.

Amino acids derived from sugar are of extensive family of peptidomimetics "(Baron et al., 2004; Chakraborty et al., 2004)", an important sub-class of which incorporate an α-amino acid with a carbohydrate has anomeric effect. Such sugar amino acids may form spiro derivatives, some of which have been demonstrated to possess significant biological activity. For instance, the formula and crystal structure of (2'*S*,3a*R*,6*S*,6a*R*)-2,2,6-trimethyldihydro-3a*H*-spiro[furo[3,4-*d*][1,3]dioxole-4,2'-piperazine]-3',6'-dione (**50**) are shown in Figs. 41 and 42 "(Watkin et al., 2004)". This molecule show hydrogen bonds between N-H….O=C groups and are shown in crystal packing diagram, viewed along the *c* axis as dashed lines (Fig. 43).

**Figure 41.** Formula structure of compound **50**.

**Figure 42.** Crystal structure of compound **50** (Green: C, blue: N and red: O atom).

**Figure 43.** Crystal packing diagram of **50**.

230 Recent Advances in Crystallography

**Figure 39.** Formula structure of **49**.

**Figure 40.** Crystal structure of **49**.

**Figure 41.** Formula structure of compound **50**.

N

O

Me

O

N

Me

Me

Me

O O

O

O

N N

<sup>O</sup> Me

Amino acids derived from sugar are of extensive family of peptidomimetics "(Baron et al., 2004; Chakraborty et al., 2004)", an important sub-class of which incorporate an α-amino acid with a carbohydrate has anomeric effect. Such sugar amino acids may form spiro derivatives, some of which have been demonstrated to possess significant biological activity. For instance, the formula and crystal structure of (2'*S*,3a*R*,6*S*,6a*R*)-2,2,6-trimethyldihydro-3a*H*-spiro[furo[3,4-*d*][1,3]dioxole-4,2'-piperazine]-3',6'-dione (**50**) are shown in Figs. 41 and 42 "(Watkin et al., 2004)". This molecule show hydrogen bonds between N-H….O=C groups and are shown in crystal packing diagram, viewed along the *c* axis as dashed lines (Fig. 43).

O

Me

NH

O

HN

O

O O

<sup>O</sup> <sup>N</sup>

O

N

Me

Another interesting spiro linked barbituric acid to the cyclopentane ring moiety (spironucleoside) possessing of hydroxyl and hydroxymethyl groups is (3*S*,2*R*)-3-hydroxy-2 hydroxymethyl-7,9-diazaspiro[4.5]decane-6,8,10-trione (**51**) (Figs. 44 and 45). Crystal structure of **51** shows *trans* stereochemical relationship of the two substituents hydroxyl and hydroxymethyl on cyclopentane ring moiety. The barbituric acid ring is almost planar, while the cyclopentane moiety adopts the C3'-*endo*-type conformation. Molecules of **51** interconnected by a two-dimensional network of hydrogen bonds build layers parallel to the *ab* plane. The hydrogen bond data for **51** is outlined at Table 14 "(Averbuch-Pouchot et al., 2002)".

**Figure 44.** Formula structure of **51**.

**Figure 45.** Crystal structure of **51**.


Symmetry codes: (iv) *x*, *y*−1, *z*; (v) *x*, *y*+1, *z*; (vii) *x*−1, *y*, *z*.

**Table 14.** Hydrogen-bond geometry in **51** (Å, º).

Hydantoins are very useful compounds due to their pharmaceutical behaviour such as; antitumor "(Kumar et al., 2009)", anticonvulsant "(Sadarangani et al., 2012)" and antidiabetic activity "(Hussain et al., 2009)". In the molecules of **52** and **53** (Figs. 46 and 47), the atoms in the hydantoin ring are coplanar. The crystal structures of **52** and **53** are stabilized by intermolecular N—H O=C hydrogen bonds. The hydrogen bond lengthes and angles for **52** and **53** are summarized at Table 15. Crystal packing diagram of these molecules show the molecules are centrosymmetric dimer forms. The dihedral angle subtended by the 4-chloroand 4-bromophenyl groups with the plane passing through the hydantoin unit are 82.98(4)° and 83.29(5)°, respectively. The cyclohexyl ring in both molecules adopts an ideal chair conformation and methyl group in an equatorial position "(Kashif et al., 2009)".


Symmetry code: (i) -x + 1;-y + 1;-z + 1.

232 Recent Advances in Crystallography

**Figure 44.** Formula structure of **51**.

**Figure 45.** Crystal structure of **51**.

Symmetry codes: (iv) *x*, *y*−1, *z*; (v) *x*, *y*+1, *z*; (vii) *x*−1, *y*, *z*. **Table 14.** Hydrogen-bond geometry in **51** (Å, º).

the cyclopentane moiety adopts the C3'-*endo*-type conformation. Molecules of **51** interconnected by a two-dimensional network of hydrogen bonds build layers parallel to the *ab* plane. The

O

D—H A D—H H A D A D—H A

Hydantoins are very useful compounds due to their pharmaceutical behaviour such as; antitumor "(Kumar et al., 2009)", anticonvulsant "(Sadarangani et al., 2012)" and antidiabetic activity "(Hussain et al., 2009)". In the molecules of **52** and **53** (Figs. 46 and 47), the atoms in the hydantoin ring are coplanar. The crystal structures of **52** and **53** are stabilized by intermolecular N—H O=C hydrogen bonds. The hydrogen bond lengthes and angles for **52** and **53** are summarized at Table 15. Crystal packing diagram of these molecules show the molecules are centrosymmetric dimer forms. The dihedral angle subtended by the 4-chloroand 4-bromophenyl groups with the plane passing through the hydantoin unit are 82.98(4)° and 83.29(5)°, respectively. The cyclohexyl ring in both molecules adopts an ideal chair

O11—H12 O6v 0.81 2.00 2.809 (2) 173 N7—H8 O10iv 0.86 1.99 2.840 (2) 170 N9—H9 O2vii 0.85 2.04 2.8620 (10) 161

conformation and methyl group in an equatorial position "(Kashif et al., 2009)".

OH

OH

O

hydrogen bond data for **51** is outlined at Table 14 "(Averbuch-Pouchot et al., 2002)".

HN

HN

O

**Table 15.** Hydrogen-bond geometry in **52** (Å, º).

**Figure 46.** Formula structures of **52** and **53**.

**Figure 47.** Crystal structures of **52** (top) and **53** (bottom).

Dihydropyridine are interesting and important systems because of their exceptional properties as calcium channel antagonists "(Si et al., 2006)" and as powerful arteriolar vasodilators "(Kiowski et al., 1990)". 4',4'-Dimethyl-2-methylsulfanyl-3,4,5,6,7,8 hexahydropyrido-[2,3-*d*]pyrimidine-6-spiro-1'-cyclohexane-2',4,6'-trione, (**54**), has a markedly polarized molecular electronic structure, and the molecules are linked into a three-dimensional framework by a combination of N–H O, C–H O and C–H л hydrogen bonds (Table 16). Two independent N–H O hydrogen bonds generate a onedimensional substructure in the form of a chain of rings; these chains are linked into sheets by the C–H O hydrogen bonds, and the sheets are linked by C–H л hydrogen bonds. Crystal packing diagram of **54** show four types of centrosymmetric ring. "(Low et al., 2004)" (Fig. 48). Compound **54** can exist in two zwitterionic forms of **54I** and **54II** (Scheme 11). For example, the bond lengths of N3–C4 and C4–O4 are both long for their types, the C4–C4A and C4A–C8A bonds are too similar in length to be characterized as single and double bonds, respectively. Also, the C8A–N8 bond, involving a threecoordinate N atom, is much shorter than the C8A–N1 bond, which involves a twocoordinate N atom. These observations, taken together, effectively preclude the polarized form (**54I**) as an effective contributor to the overall molecular electronic structure, instead pointing to the importance of the polarized vinylogous amide form (**54II**) "(Low et al., 2004)".

**Scheme 11.** Zwitterionic forms of **54**.

**Figure 48.** Crystal structure of **54**.


Symmetry codes: (i) 1 - x; 1 - y; 1 - z; (ii) -x; 1 - y; -z; (iii) -x; 2 - y;-z; (iv) 1 -x;-y;-z. Cg1 is the centroid of the pyrimidinone ring.

**Table 16.** Hydrogen-bonding geometry (Å, °) for **54**.

## **3. Conclusion**

234 Recent Advances in Crystallography

N

H

**Scheme 11.** Zwitterionic forms of **54**.

**Figure 48.** Crystal structure of **54**.

MeS N N

H

O

O

N

H

MeS N N

O

O

2004)".

dimensional substructure in the form of a chain of rings; these chains are linked into sheets by the C–H O hydrogen bonds, and the sheets are linked by C–H л hydrogen bonds. Crystal packing diagram of **54** show four types of centrosymmetric ring. "(Low et al., 2004)" (Fig. 48). Compound **54** can exist in two zwitterionic forms of **54I** and **54II** (Scheme 11). For example, the bond lengths of N3–C4 and C4–O4 are both long for their types, the C4–C4A and C4A–C8A bonds are too similar in length to be characterized as single and double bonds, respectively. Also, the C8A–N8 bond, involving a threecoordinate N atom, is much shorter than the C8A–N1 bond, which involves a twocoordinate N atom. These observations, taken together, effectively preclude the polarized form (**54I**) as an effective contributor to the overall molecular electronic structure, instead pointing to the importance of the polarized vinylogous amide form (**54II**) "(Low et al.,

N

H

O

H

**54 54I**

O

**54II**

MeS N N

H

O

O

O

In summary, X-ray single crystal diffraction analysis of the some helicenes and other helix molecules were discussed. In continuation, the crystal structure of some organic and organometallic compounds consists of intra- and/or intermolecular hydrogen bond were described. Finally, crystal structures of some new spiro compounds were analyzed.

### **Author details**

Nader Noroozi Pesyan *Urmia University, Iran* 

## **Acknowledgement**

The author gratefully acknowledge financial support by Research Council of Urmia University

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**Section 4** 
